BALSA / ELSA

FASTQ to Variants: WGS in 4 hours on a node

BALSA / ELSA is an economic, fast and accurate solution for the secondary analysis of next generation sequencing data. 

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Speed

BALSA / ELSA* can process a 50-fold whole genome sequence (WGS) sample from raw reads to variants, including single nucleotide polymorphism (SNP), and insertion and deletion (INDEL), in about 4 hours, or just 10 minutes for a 200-fold whole exome sequence (WES) sample.

Functionalities

- WGS alignment and variant calling
- WES alignment and variant calling
- Amplicon sequencing 
- Tumor pairs
- Variant outputs in VCF format
- Alignment outputs in BAM or SNAPSHOT formats 

* BALSA requires GPU support while ELSA is a version of BALSA optimized to run on multi-core CPUs only.

Time Consumption Comparison of BALSA/ELSA with other pipelines

Technology

BALSA / ELSA takes advantage of highly optimized indexing and parallel algorithms to effectively exploit a GPU and CPU SIMD, respectively, to speed up processes like alignment, score recalibration, INDEL realignment, de-duplication and variant calling.

A 16-genotype model is incorporated to support the calling of SNPs and INDELs. Validation of the final results with the NIST Genome In A Bottle standard demonstrates that BALSA / ELSA's analysis pipeline has the highest combined sensitivity and precision.

ELSA
  50x WGS (hr) 210x WES (min)
AWS c3.8xlarge
32 vCPUs
4.30 13.25
E5-2620v2 * 2
12 cores, 2.0GHz
7.36 16.62
E5-2637v2 * 2
8 cores, 3.5GHz
8.60 22.52
BALSA
  50x WGS (hr) 210x WES (min)
E5-2620v2
6 cores + 1 GPU
5.67 18.62
IBM Power8
6 cores + 1 GPU
4.85 14.55
i7-3930K
6 cores + 1 GPU
5.20 14.21


BALSA / ELSA Diagram

Hardware Requirements

BALSA can run at a minimum hardware requirement of 6- core CPU and an NVIDIA GPU with 4GB RAM, while ELSA needs a minimum 16-core CPU with 64GB RAM.

See the table below to find out which version is more suitable for your current hardware.

Licensing

Different kinds of licensing are available to suit your infrastructure. See the table below.


  ELSA BALSA-Power8 BALSA-x86
Minimum Hardware
Requirement
8-core CPU
64GB RAM
Power8 S814L
64GB RAM
NVIDIA GPU with 4GB RAM
6-core CPU
64GB RAM
NVIDIA GPU with 4GB RAM
Recommended Hardware Requirement 16-core CPU
96 GB RAM
Power8 S824L
96 GB RAM
NVIDIA GPU with 6GB RAM
12-core CPU
96 GB RAM
NVIDIA GPU with 6GB RAM



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Other Links

BALSA / ELSA Academic Paper

BALSA / ELSA Benchmark Results on GIAB

BALSA / ELSA Documentation

* Luo R, Wong Y, Law W, Lee L, Cheung J, Liu C, Lam T. (2014) BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU.PeerJ 2:e421 dx.doi.org/10.7717/peerj.421